The next season, his fourth in Florida, Boyle was traded to the Tampa Bay Lightning in exchange for a 2003 fifth-round draft pick (Martin Tůma) on January 7, 2002.[1] After completing the season with 20 points in 41 games after coming over from the Panthers, he was re-signed to a one-year contract by the Lightning on August 6, 2002.[2]

Boyle recorded 13 goals and 53 points in his first full season with the Lightning in 2002–03 before helping the team to the 2004Stanley Cup championship. Due to the 2004–05 NHL lockout, Boyle went overseas to play for Djurgårdens IF of the Swedish Elitserien. As NHL play resumed the next season, Boyle continued to produce with a 15-goal, 53-point season in 2005–06. He recorded his first career NHL hat-trick against the New York Rangers on December 23, 2006, adding an assist for a four-point game in a 4–3 win.[3] The following season, Boyle elevated his game to career-high numbers of 20 goals, 43 assists and 63 points, good enough for Second Team All-Star honours.

Boyle suffered a major setback, however, in September 2007, injuring himself in a freak accident after a pre-season game when a skate slipped off a hook in his locker and hit him in the left wrist, severing three tendons.[4] Boyle underwent initial wrist surgery on September 23;[5] he attempted to return on October 29, but after playing his first four games of the 2007–08 season, Boyle underwent additional surgery on the injured wrist,[6] missing another 36 games. He did not make a full comeback until January 24, 2008, scoring two goals in his return,[7] and soon thereafter was re-signed to a six-year, $40 million contract extension on February 25.[8] He completed his injury-shortened campaign with 25 points in 37 games.

In his first season with the Sharks, Boyle tallied 16 goals and 57 points over 77 games, leading all team defencemen. The following season, on December 31, 2009, Boyle scored his 100th career NHL goal against the Phoenix Coyotes in a 3–2 shootout win. He finished the campaign with 15 goals and 58 points. In the opening series of the 2010 playoffs, Boyle ended game three against the Colorado Avalanche in overtime by inadvertently shooting the puck into his own net. Pressured by Avalanche forward Ryan O'Reilly, Boyle attempted to ring the puck around the boards behind his net, but it was deflected by O'Reilly into the Sharks' net between Evgeni Nabokov's pad and the post.[10] Nonetheless, the Sharks won the series 4–2, winning Games 4, 5 and 6; Boyle had a point in all three games.

In the first period of the October 15, 2013, against the St. Louis Blues, Boyle was checked from behind by Maxim Lapierre into the boards, injuring his jaw and knocking him unconscious;[11] the incident led to a fight involving teammate Matt Pelech and 17 minutes worth of penalties for Andrew Desjardins. Boyle was taken off the ice via stretcher to a local hospital,[12] and would miss the following game against the Dallas Stars.[13] He returned on November 2, in a game against the Phoenix Coyotes, scoring a goal in a shootout loss. After the conclusion of the 2013–14 season, Sharks general manager Doug Wilson announced that pending free agent Boyle would not be returning to San Jose for the 2014–15 season.[14] On June 5, the Sharks traded his rights to the New York Islanders for a conditional 2015 fifth-round pick.[15]

Unable to come to terms with the Islanders, Boyle opted to head to free agency, and on July 1, 2014, he signed a two-year contract with the New York Rangers.[16]

On October 5, 2016, Boyle announced his retirement from the NHL. Boyle scored 164 goals and 605 points over 1,093 NHL games with four teams. In his retirement statement Boyle said that "I've been fortunate and blessed to have had the opportunity to do what I most love to do. All I wanted to do as a young boy was have the opportunity to play ONE game in the NHL. Over a thousand games later, this whole experience seems surreal. I want to thank all four organizations for the opportunity, my teammates and the FANS for this amazing run that I will cherish forever." Boyle stated that he will live in the San Jose area with his family.[17]